Boris Johnson has urged the government to intervene in a funding dispute over the London Underground after alleging that the network's struggling contractor, Tube Lines, will pay out £1.1bn in secondment fees to its shareholders.

The London mayor has asked the transport secretary, Lord Adonis, to approach Tube Lines's owners and pressure them to forgo their fees for the next seven-and-a-half years. Tube Lines, a public private partnership contractor, is owned by Bechtel, a US project management firm, and Amey a UK-based consultancy, who charge the company fees to use its employees.

According to Johnson the co-owners are due to receive a profit of about £400m from these fees by 2017, out of a total of £1.1bn since the controversial PPP contract began in 2002. The mayor's transport authority, Transport for London, is facing a £400m funding shortfall in payments to Tube Lines over the next seven years and Johnson cited the management fees as an appropriate solution to a financial crisis at TfL. Alternatively, Johnson said, the government could provide the funds through the taxpayer.

"You have an obligation to intervene immediately to make good the likely funding shortfall faced by London to ensure that the Tube upgrades are delivered in full, either by funding the shortfall from government resources or by persuading Tube Lines's shareholders to give up their extraordinary returns in the light of their abject failings," he wrote.

TfL is claiming that the next seven-and-a-half-years' work on the Northern, Jubilee and Piccadilly lines – which are maintained by Tube Lines – should cost £4bn. However, an independent arbiter has priced the work at £4.4bn in a draft ruling, leaving TfL with a potential funding gap of £400m. Tube Lines's funding hole is even bigger, because it has argued that the work should cost £5.75bn – leaving the company with a potential shortfall of £1.35bn.

The Department for Transport has refused to give more cash to TfL, which received a funding settlement of £40bn for 2010-2017, including TfL's contribution to the £16bn Crossrail project that will drive a new underground railway through central London. A source close to Tube Lines accused the mayor of "hypocrisy" because TfL also pays out secondment fees to private contractors after taking over the largest underground PPP contractor, Metronet, in 2007. According to Tube Lines, TfL has paid Canadian engineering firm Bombardier £88m in similar fees for upgrading the Victoria line. "It is hypocritical to attack us on this when they pay out such high fees for the Victoria Line."

TfL has argued that the Bombardier fees are a legacy of a contract that it inherited after Metronet's collapse.

[After this story was published, TfL contacted the Guardian to say that it has not paid the £88m referred to: "Over 70% of these fees had already been paid under Metronet and before the transfer to TfL". Having inherited these arrangements, "we have absolutely no interest in defending such payments," it said.]

• This article was updated on 8 February 2010 to include TfL's response to the £88m fees accusation.